
import clusterAnalysis.BasicClusterNetworkFigure;
import clusterAnalysis.ClusterIntersections;
import clusterAnalysis.ClusterStats;
import clusterAnalysis.HIVProtInteractionStats;
import clusterAnalysis.MinetClusterAnalysis;
import clusterAnalysis.OutputMaxExpStats;
import com.sun.org.apache.bcel.internal.generic.AALOAD;
import controllers.ControllerStatistics;
import db.HivDbIntegration.IntersectionSummary;
import db.HivDbIntegration.MakeNetworkOutput_separate;
import db.HivDbIntegration.MakeNetworkOutput_together;
import db.MakeClusterIntersectionsTable;
import db.MakeClustersTable_individual;
import db.MakeClustersTable_together;
import db.MakeDB;
import db.MakeSwissProtLookup;
import functionalEnrichment.MakeEnrichmentTable;
import functionalEnrichment.semanticSimilarity.MakeGeneSetsForAnalysis;
import functionalEnrichment.semanticSimilarity.semanticSimilarityCalculator.SemanticSimilarityProgram;
import functionalEnrichment.semanticSimilarity.semanticSimilarityCalculator.units.OntologyType;
import hivInteractions.HivInteractionEnrichment;
import hivInteractions.MakeMainHivNetwork;
import java.io.IOException;
import java.util.logging.Level;
import java.util.logging.Logger;
import jsc.independentsamples.MannWhitneyTest;
import jsc.tests.H1;
import outToR.SeparateClustOutput;
import outToR.OutputForMinet;
import outToR.TogetherClustOutput;
import regulatoryInteractionsStats.yeast.PPIStats;
import regulatoryInteractionsStats.yeast.SemanticSimStats;
import regulatoryInteractionsStats.yeast.bioJava.DoAlignments;
import regulatoryNetworks.GenePairTest;
import regulatoryNetworks.GoTermPairTest;
import regulatoryNetworks.RegulatoryNetwork;
import units.CellType;
import units.MonkeyType;

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */

/**
 *
 * @author jamie
 */
public class Main {

    public static void main(String[] args) {
//        RegulatoryNetwork rn = new RegulatoryNetwork();
//        rn.outputAllNetworks();

        ControllerStatistics cs = new ControllerStatistics();
        cs.run(MonkeyType.M, CellType.P);
        cs.run(MonkeyType.M, CellType.L);
        cs.run(MonkeyType.A, CellType.P);
        cs.run(MonkeyType.A, CellType.L);
        cs.getHandle().closeConnection();

//        GenePairTest genePairTest = new GenePairTest();
//        genePairTest.runRandomTest(10000, OntologyType.BIOLOGICAL_PROCESS);
//        genePairTest.runTest(OntologyType.BIOLOGICAL_PROCESS);
//        genePairTest.runTest(OntologyType.BIOLOGICAL_PROCESS, 10000);
//        try {
//            genePairTest.outputGoTermPairPValues(10000);
//        } catch (IOException ex) {
//            Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
//        }
    }
}
